Magnesium in PDB 7u0y: Crystal Structure of Pepper Rna Aptamer in Complex with HBC599 Ligand and Fab BL3-6

The structure of Crystal Structure of Pepper Rna Aptamer in Complex with HBC599 Ligand and Fab BL3-6, PDB code: 7u0y was solved by H.C.Rees, J.A.Piccirilli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.67 / 2.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.247, 96.071, 148.165, 90, 90, 90
R / Rfree (%)	21.9 / 25.5

The binding sites of Magnesium atom in the Crystal Structure of Pepper Rna Aptamer in Complex with HBC599 Ligand and Fab BL3-6 (pdb code 7u0y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Pepper Rna Aptamer in Complex with HBC599 Ligand and Fab BL3-6, PDB code: 7u0y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Pepper Rna Aptamer in Complex with HBC599 Ligand and Fab BL3-6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Pepper Rna Aptamer in Complex with HBC599 Ligand and Fab BL3-6 within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg302 b:90.1 occ:1.00 O R:HOH423 1.8 91.9 1.0 OP2 R:A11 2.0 82.9 1.0 O R:HOH463 2.1 116.7 1.0 O R:HOH455 2.3 76.8 1.0 O R:HOH436 2.4 88.5 1.0 O R:HOH457 2.6 88.3 1.0 O R:HOH419 2.9 89.7 1.0 P R:A11 3.3 104.2 1.0 O R:HOH473 3.5 77.8 1.0 O5' R:A11 3.8 93.5 1.0 O4 R:U13 4.0 90.7 1.0 OP1 R:A11 4.0 108.1 1.0 O R:HOH440 4.1 93.7 1.0 H3' R:C10 4.1 118.1 1.0 O R:HOH471 4.2 93.1 1.0 H62 R:A12 4.4 100.9 1.0 O3' R:C10 4.5 97.3 1.0 H8 R:A11 4.6 93.7 1.0 O R:HOH420 4.6 80.9 1.0 N7 R:A12 4.6 80.3 1.0 OP1 R:C10 4.6 93.0 1.0 OP1 R:G18 4.6 82.7 1.0 OP2 R:A12 4.7 96.5 1.0 H3' R:A11 4.8 113.0 1.0 C3' R:C10 4.8 98.4 1.0 O5' R:C10 4.9 90.3 1.0 C8 R:A11 4.9 78.1 1.0 O R:HOH458 5.0 78.8 1.0 N7 R:A11 5.0 77.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Pepper Rna Aptamer in Complex with HBC599 Ligand and Fab BL3-6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Pepper Rna Aptamer in Complex with HBC599 Ligand and Fab BL3-6 within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg303 b:86.8 occ:1.00 OP2 R:U53 1.8 81.0 1.0 OP2 R:C52 1.9 73.9 1.0 O R:HOH409 2.0 63.5 1.0 O R:HOH402 2.0 72.8 1.0 N7 R:G54 2.0 71.5 1.0 O R:HOH450 2.2 58.5 1.0 C8 R:G54 2.8 68.8 1.0 H8 R:G54 2.9 82.6 1.0 H5'' R:C52 3.2 93.1 1.0 C5 R:G54 3.2 74.7 1.0 P R:U53 3.3 78.2 1.0 H5 R:U53 3.3 85.9 1.0 P R:C52 3.3 75.9 1.0 H3' R:C52 3.4 99.6 1.0 O6 R:G54 3.8 80.9 1.0 O3' R:C52 3.8 78.0 1.0 C6 R:G54 3.9 74.5 1.0 C5' R:C52 4.0 77.5 1.0 O5' R:C52 4.0 78.7 1.0 OP1 R:C52 4.0 83.5 1.0 C3' R:C52 4.0 83.0 1.0 O5' R:U53 4.1 76.3 1.0 H6 R:U53 4.1 89.8 1.0 C5 R:U53 4.1 71.6 1.0 N9 R:G54 4.1 68.2 1.0 C4 R:G54 4.3 69.0 1.0 OP1 R:U53 4.3 89.2 1.0 O3' R:A51 4.4 69.9 1.0 C6 R:U53 4.5 74.8 1.0 C4' R:C52 4.6 82.1 1.0 H5' R:C52 4.7 93.1 1.0

H.C.Rees, W.Gogacz, N.S.Li, D.Koirala, J.A.Piccirilli. Structural Basis For Fluorescence Activation By Pepper Rna. Acs Chem.Biol. V. 17 1866 2022.
ISSN: ESSN 1554-8937
PubMed: 35759696
DOI: 10.1021/ACSCHEMBIO.2C00290